In unstable market conditions and a tough competitive environment, economic security diagnostics is an important tool for identifying reserves and opportunities to increase the efficiency of trading enterprises. A reliable assessment of the economic condition of a trade enterprise is crucial for forming correct conclusions and making adequate management decisions. The purpose of the article is to generalize the methodological tools for assessing the economic security of business processes of commercial enterprises and identify the features of its practical application. The article analyzes the existing methodological approaches to assessing the level of economic security of an enterprise. Assessment of the level of economic security is not identical to estimation of level of economic safety of business processes of the enterprise, so the author’s approach to the assessment of economic security of business processes of a trade enterprise. A cost-based approach to a comprehensive assessment of the level of economic security of business processes of a trade enterprise is justified. In addition, the assessment of the level of economic security of business processes of trade enterprises, in our opinion, should be carried out at certain stages, which are characterized by complexity, consistency, the use of tools for making calculations, taking into account the influence of internal and external factors. In the article the indicators for assessing business processes from a position of ensuring economic security of commercial enterprises, the analysis of which will allow to assess the state of enterprise economic security and its potential development. These indicators influence or as stimulants, increasing which enhances the security level of an enterprise, or as destimulation, the growth of which leads to a decrease in its level. The author’s model of assessing the economic security of business processes of a trade enterprise is unified and complex and allows you to thoroughly, taking into account the complexity of the hierarchical system of economic security, to make calculations and make effective management decisions to ensure the economic security of the enterprise.